Semantic Web Technology in Support of Bioinformatics f or Glycan Expression Amit Sheth Large Scale Distributed Information Systems (LSDIS) lab, Univ. of Georgia and Semagix, Inc. W3C workshop on Semantic Web for Life Sciences , October 28, 2004, Cambridge MA Thanks to Will York, Christopher Thomas, Satya Sanket Sahoo
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Semantic Web Technology in Support of Bioinformatics for Glycan Expression Amit Sheth Large Scale Distributed Information Systems (LSDIS) lab, Univ. of.
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Semantic Web Technology in Support of Bioinformatics for
Glycan Expression Amit Sheth
Large Scale Distributed Information Systems (LSDIS) lab, Univ. of Georgia
and Semagix, Inc.
W3C workshop on Semantic Web for Life Sciences, October 28, 2004, Cambridge MA
Thanks to Will York, Christopher Thomas, Satya Sanket Sahoo
NIH Integrated Technology Resource for Biomedical Glycomics
Complex Carbohydrate Research Center The University of Georgia
Biology and Chemistry• Michael Pierce – CCRC (PI)• Al Merrill - Georgia Tech• Kelley Moremen - CCRC• Ron Orlando - CCRC• Parastoo Azadi – CCRC• Stephen Dalton – UGA Animal
Science
Bioinformatics and Computing•Will York - CCRC•Amit Sheth, Krys Kochut, John Miller; UGA Large Scale Distributed Information Systems Laboratory
Quick Take• Comprehensive and deep domain ontology
– GlycO
• Process ontology to go beyond provenance– ProGlycO
• Semantic Annotation of Scientific data– Textual– Experimental, machine-generated, non-textual
• Tool for ontology visualization, querying,…• All open source, free
Central Role of Ontology• Ontology represents agreement, represents
common terminology/nomenclature• Ontology is populated with extensive domain
knowledge or known facts/assertions• Key enabler of semantic metadata extraction from
all forms of content:–unstructured text (and 150 file formats)–semi-structured (HTML, XML) and –structured data
• Ontology is in turn the center price that enables–resolution of semantic heterogeneity –semantic integration–semantically correlating/associating objects and
documents
Types of Ontologies (or things close to ontology)• Upper ontologies: modeling of time, space, process, etc• Broad-based or general purpose ontology/nomenclatures:
Cyc, CIRCA ontology (Applied Semantics), SWETO, WordNet ;
• Domain-specific or Industry specific ontologies– News: politics, sports, business, entertainment– Financial Market– Terrorism– Pharma– GlycO– (GO (a nomenclature), UMLS inspired ontology, …)
• Application Specific and Task specific ontologies– Anti-money laundering– Equity Research– Repertoire Management
Blue: Commercial ontologies developed by Semagix or its customers; Brown: open/public ontologies from LSDIS Lab, Univ. of Georgia
Expressiveness Range: Knowledge Representation and Ontologies
Catalog/ID
GeneralLogical
constraints
Terms/glossary
Thesauri“narrower
term”relation
Formalis-a
Frames(properties)
Informalis-a
Formalinstance
Value Restriction
Disjointness, Inverse,part of…
Ontology Dimensions After McGuinness and FininOntology Dimensions After McGuinness and Finin
SimpleTaxonomies
Expressive
Ontologies
Wordnet
CYCRDF DAML
OO
DB Schema RDFS
IEEE SUOOWL
UMLS
GO
KEGG TAMBIS
EcoCyc
BioPAX
GlycOSWETO
Pharma
Ontology can be very large
Semantic Web Ontology Evaluation Testbed – SWETO v1.4 is
• Populated with over 800,000 entities and over 1,500,000 explicit relationships among them
• Continue to populate the ontology with diverse sources thereby extending it in multiple domains, new larger release due soon
• Two other ontologies of Semagix customers have over 10 million instances, and requests for even larger ontologies exist
GlycO statistics: Ontology schema can be large and complex
• 767 classes• 142 slots• Instances Extracted with Semagix Freedom:
– 69,516 genes (From PharmGKB and KEGG)– 92,800 proteins (from SwissProt)– 18,343 publications (from CarbBank and MedLine)– 12,308 chemical compounds (from KEGG)– 3,193 enzymes (from KEGG)– 5,872 chemical reactions (from KEGG)– 2210 N-glycans (from KEGG)
GlycO
• is a focused ontology for the description of glycomics
• models the biosynthesis, metabolism, and biological relevance of complex glycans
• models complex carbohydrates as sets of simpler structures that are connected with rich relationships
GlycO taxonomyThe first levels of the GlycO taxonomy
Most relationships and attributes in GlycO
GlycO exploits the expressiveness of OWL-DL.Cardinality constraints, value constraints, Existential and Universal restrictions on Range and Domain of properties allow the classification of unknown entities as well as the deduction of implicit relationships.
Data provenance: information regarding the ‘place of origin’ of a data element
Mapping a data element to concepts that collaboratively define it and enable its interpretation – Semantic Annotation
Data provenance paves the path to repeatability of data generation, but it does not enable: Its (machine) interpretability Its computability (e.g., discovery)
Semantic Annotations make these possible.
Identified and quantified
peptides
Specific cellularprocess
Lectin
Collection of N-glycan ligands
Collection ofBiosynthetic enzymes
Discovery of relationship between biological Discovery of relationship between biological entitiesentities
Fragment ofSpecific protein
GlycOProglycO
Gene Ontology (GO)
Genomic database (Mascot/Sequest)
The inference: instances of the class collection of Biosynthetic enzymes (GNT-V) are involved in the specific cellular process (metastasis).
p
r
o
c
e
s
s
Dimensions of expressiveness
complexitybivalent Multivalued
discretecontinu
ous
Degre
e o
f Ag
reem
ent
Info
rmal
Sem
i-Form
al
Form
al
Expressiveness
XMLRDF
FOL withfunctions
Current Semantic
Web Focus
Futureresearch
Cf: Guarino, Gruber
RDFS/OWL
FOL w/o functions
The downside
• That a structure is not valid according to the ontology could just mean that it is a new kind of structure that needs to be incorporated
• That a substance can be synthesized according to one pathway does not exclude the synthesis through another pathway
Man9GlcNAc2
Glycan
is a
Glycosyl Transferase
is a
synthesizes
May Synthesize
Mannose
contains
transfers
May Synthesize
Lipid-mannosyl transferase
Probabilistic Relationships
For more information
• http://lsdis.cs.uga.edu– Especially see Glycomics project– SWETO ontology